A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation.

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Ten aliquots of a single stool sample collected from a healthy human volunteer were either pretreated by differential centrifugation (DC; N=5) or not centrifuged (NC; N=5). Protein extracts were then processed by filter-aided sample preparation, single-run liquid chromatography and high-resolution mass spectrometry, and peptide identification was carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform. The dataset described here is also related to the research article entitled \"Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota\" published in Proteomics (Tanca et al., 2015), [1].", "claims": [{"id": "claim-data-access", "statement": "ProteomeXchange Consortium, dataset identifier PXD001573 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001573", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26306325", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "ProteomeXchange Consortium, dataset identifier PXD001573 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001573"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used Percolator for peptide validation at an FDR below 1% based on peptide q-values, and the source data are accessible through the ProteomeXchange Consortium via the PRIDE partner repository under dataset identifier PXD001573.", "kind": "quantitative", "target": {"value": 1.0, "unit": "per cent", "tolerance": null, "source": "Peptide identification was performed using Proteome Discoverer (version 1.4.1; Thermo Scientific), with a workflow consisting of the following nodes (and respective parameters): Spectrum Selector for spectra pre-processing (precursor mass range: 350–5000 Da; S/N Threshold: 1.5), Sequest-HT as search engine (Protein Database: see below; Enzyme: Trypsin; Max. missed cleavage sites: 2; Peptide length range 5–50 amino acids; Max. Delta Cn: 0.05; Precursor mass tolerance: 10 ppm; Fragment mass tolerance: 0.02 Da; Static modification: cysteine carbamidomethylation; Dynamic modification: methionine oxidation), and Percolator for peptide validation (FDR<1% based on peptide q-value)."}, "evidence": [{"asset": "source:pmid:26306325", "locator": "sections[10] \"Data analysis\" paragraph 2", "quote": "Peptide identification was performed using Proteome Discoverer (version 1.4.1; Thermo Scientific), with a workflow consisting of the following nodes (and respective parameters): Spectrum Selector for spectra pre-processing (precursor mass range: 350–5000 Da; S/N Threshold: 1.5), Sequest-HT as search engine (Protein Database: see below; Enzyme: Trypsin; Max. missed cleavage sites: 2; Peptide length range 5–50 amino acids; Max. Delta Cn: 0.05; Precursor mass tolerance: 10 ppm; Fragment mass tolerance: 0.02 Da; Static modification: cysteine carbamidomethylation; Dynamic modification: methionine oxidation), and Percolator for peptide validation (FDR<1% based on peptide q-value)."}, {"asset": "source:pmid:26306325", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We present a human gut metaproteomic dataset deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001573."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used Percolator for peptide validation at an FDR below 1% based on peptide q-values, and the source data are accessible through the ProteomeXchange Consortium via the PRIDE partner repository under dataset identifier PXD001573.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26306325"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD001573"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD001573"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26306325", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.07.014", "sha256": "sha256:040a676d6b4b379fc3862c21647092a5a20b050b4ea4c48f8ef457757311d36b", "bytes": 9108, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.07.014", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4536287", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001573", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD001573", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001573", "version": null, "note": "ProteomeXchange Consortium, dataset identifier PXD001573 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001573", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "ProteomeXchange Consortium, dataset identifier PXD001573 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001573", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Enrichment or depletion? 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